1. Presumably you found used copy of Advance Wars: Dual Strike or Days of Ruin since those are the only Advance Wars games you can play on the 3DS (and only because they are DS games and 3DS can play regular DS games)
2. Yes, games bought on the eShop don't need a physical game in any way. As long as you have the money and memory, you can get it.

I haven't played as many of the big 3DS titles as some people, but I'd say some good games to play would be:
-Luigi's Mansion: Dark Moon: A really great puzzle-y game that expands heavily on the original GCN game
-Kirby Triple Deluxe: One of the best Kirby games in a long while (and I've heard the follow-up, Robobot, is even better).
-Super Mario 3D Land: A weird 3D version of...the old 2D Mario games. Pretty high quality.
-Metroid: Samus Returns: A good 2D Metroid game, nuff said
-Pushmo and Stretchmo: High quality puzzle games on the eShop
-Steamworld Dig 1 and 2: Excellent 2d platformers that play like a mix of Metroid and Terraria. Also eShop.
-Steamworld Heist: Awesome strategy game. eShop.

Bioshock is 10 years old. Let's play through its horrific environment and see why its so beloved!LeT's PlAy BIOSHOCK < Link to LP